RihaoQu

Hi, this depends on your goal of analysis. If you would like to compare the structure of the gene graph (or gene trajectories) between two different conditions, you will need...

Hi, the following code might be helpful to highlight the location of specific gene markers. ```r #After getting the gene embedding and extracting gene trajectories gene_labels

Yes, the gene trajectories cannot be directly colored by cell types since they do not match cell barcodes. As an alternative, you can correspond each trajectory to specific cell populations...

Hi, if you are using Seurat v5, you can try to update the object by ```r library(SeuratObject) data_S = SeuratObject::UpdateSeuratObject(data_S) ``` Then, change the following line in the first code...